1bxi

CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9


Structural alignment of the immunity protein 9 (Im9, 1bxi, colored yellow), evolved variant of the immunity protein 9 R12-2 (lime, 3gkl), and immunity protein 7 (Im7, colored blue , 7cei) reveals their structural identity. However, when the immunity proteins-bound colicins within their complexes were aligned, they demonstrate somewhat different picture. The Im9 and Im7 are differ more in their binding configurations (19°, with Tyr54-Tyr55 as the pivot), while the variant R12-2 is in an intermediate configuration between Im9 and Im7. Of note, in the variant R12-2 (3gkl) and Im9 (1bxi) there are Tyr54 and Tyr55, while in the Im7 (7cei) Tyr55 and Tyr56 are homologous to them. The most prominent differences are in the loop between helices α1 and α2 in Im9 (yellow, labeled in black) and evolved variant R12-2 (lime, labeled in black). This loop consists of three mutations: N24D, T27A, and S28T in variant R12-2. We can see the deviations in the relative position of helices α1 and α2, in the loop's backbone and in the side chains of residues 24, 26 and 28.

 Comparison of the different Im-colicin complexes reveals changes in the binding configuration of the evolved variants which increase affinity toward ColE7 by re-aligning pre-existing Im9 residues. Glu30 of Im9 (1bxi, colored yellow) forms double salt bridge with Arg54 of ColE9 (orange), whereas Asp51 have not direct side chain–side chain interactions. Asp31 of Im7 (blue) which is corresponding to Im9 Glu30 is involved in cluster of salt bridge bonds to Arg520 and Lys525 of ColE7 (darkmagenta), while Asp52 of Im7 (corresponding to Im9 Asp51) is within hydrogen bond distance to Thr531 and Arg530 of ColE7 (7cei). Glu30 in the variant R12-2 (lime) is shifted and forms a <scene name='3gkl/Active_site/8'>double salt bridge to <font color='magenta'>Arg520 of ColE7 (magenta). <font color='lime'>Asp51 is within hydrogen bond distance to <font color='magenta'>Thr531 of ColE7 (3gkl). However, the side chains of <font color='magenta'>Lys525 and Arg530, which are very important in salt bridge contacts with Glu30 and Asp51, respectively, in the structure of the ColE7–Im7 complex have a different conformation that eliminates these contacts in evolved variant R12-2.

About this Structure
1BXI is a 2 chains structure of sequences from Escherichia coli. Full crystallographic information is available from OCA.